I used to work at a GM Dealer in the service department. There is no doubt if they think it is related they will try and blame it on your aftermarket parts. But don't think the dealer is just trying to get out of fixing things. The dealers take the money from you or General Motors corporate and they don't really care where it comes from. So if they can warranty it they will. And I don't see any reason the big three would affect any part of your warranty unless a loose wire resulted.
Also there is a law in place that protects consumers, stating that the manufacturer must prove your modification caused the failure to refuse a repair under warranty. So you are protected by laws as well. If your modification didn't cause the failure you have nothing to worry about.